High-quality reference genome for an arid-adapted mammal, the banner-tailed kangaroo rat (Dipodomys spectabilis)

Abstract

AbstractKangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semi-arid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (D. spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (D. ordii and D. stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (Ne) and linking these patterns to the species’ current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.Significance statementKangaroo rats in the genus Dipodomys occur in a wide variety of habitat types, ranging from scrublands to arid deserts, and are increasingly impacted by habitat fragmentation with populations of many species in strong decline. To facilitate population and conservation genomic studies of Dipodomys species, we generated the first reference genome assembly for the extensively studied banner-tailed kangaroo rat (D. spectabilis) from long read PacBio sequencing data. The genome assembly presented here will serve as a valuable resource for studies of Dipodomys species—which have long served as ecological and physiological models for the study of osmoregulation—comparative genomic surveys of mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.